The UK's most respected independent tax and spend monitor, the Institute for Fiscal Studies, said today the changes brought in by the comprehensive spending review would "clearly" hit the poorest harder than the better off and be "regressive" without the increase in the higher rate of tax introduced by Labour.

The analysts crunched both the changes in public service cuts and welfare cuts and on both reached gloomier conclusions than the government.

Progressive or regressive?

The Treasury asserted that their changes saw people shouldering more of the burden as they got richer – or were progressive. But the IFS said the government was ignoring a third of the welfare changes it was making and was producing graphs that did not stretch until 2014-5, when many of their changes were fully felt.

In addition they said the Treasury was able to claim the overall package was "progressive" only as a result of measures announced by the last Labour chancellor Alistair Darling, such as an increase in the higher rate of tax.

The acting IFS director Carl Emmerson said: "The tax and benefit changes are regressive rather than progressive across most of the income distribution. And when we add in the new measures announced yesterday this is, unsurprisingly, reinforced.

"Our analysis continues to show that, with the notable exception of the richest 2%, the tax and benefit components of the fiscal consolidation are, overall, being implemented in a regressive way."

Emmerson went on: "But large tax rises for the very rich announced by Labour lead, on the Treasury's estimates, to the overall fiscal consolidation hitting the highest income individuals most."

One of their tables showed that if households are ranked by spending rather than income, the bottom 30% of households are feeling more of the pain of deficit reduction than the top 2%.

Another analyst at the Institute, James Browne, said: "Overall, families with children seem to be the biggest losers. The poorest are losing more as a proportion of their income as a result of these changes."

Departmental cuts

The IFS also challenged Osborne's claim that the government's cuts to unprotected departments averaged 19% compared with 20% implied by Labour's plans. Labour's plans, the IFS said, would have meant cuts of 16%.

It said Osborne's figures failed to take into account the £6bn of cuts already announced this year. The coalition plans to cut spending and raise taxes by £114bn by the end of the parliament, compared with the tightening of £74bn offered by Labour in its last budget.

Schools

The thinktank calculates that the reality of the government's small real terms increase in schools spending coupled with rising classroom numbers meant that spending per pupil would fall by 2.25% over the next four years.

Even assuming a premium worth £2,400 per pupil in deprived areas and underlying funding per pupil frozen in cash terms, most pupils lose out.

The effect would mean a real-terms cut for 60% of primary and 87% of secondary school pupils. One in eight pupils in very deprived areas would receive a 5% boost in funding, but 43% of pupils in less deprived parts of the country would be hit by 5% cuts or more, the IFS said.

This would appear to explain why an internal and confidential projection drawn up by civil servants at the Department for Education suggested 40,000 teachers could lose their jobs over the course of this spending review.

The IFS also pointed out it was inconsistent for the government to model the effect of the pupil premium across households but to insist it was incapable of doing the same modelling for other changes.

In an article for the Guardian's Comment is Free site, the shadow education secretary Andy Burnham says the Treasury's green book shows the pupil premium will "sit within" a schools budget that will see per pupil funding falling in real terms.

Council tax benefit

Local authorities instead of central government will calculate council tax rebates to poorer households under plans that will also cut spending by 10%, saving £490m a year from 2013-4. At the moment Whitehall decides how this fiendishly complex benefit should be paid.

People on low incomes, pensioners and single people could all find they are eligible for smaller rebates, depending on where they live. The government's only message is to protect the poorest households. The IFS said the measure failed many of the government's own tests. Aside from the cries of postcode lottery, it would become more difficult for claimants to judge their entitlement with the knock on effect of deterring unemployed people from taking work.

It would also give councils scope to skew the rebates to particular groups. Combined with caps on housing benefit and significant hikes in social housing rents, poorer families could be chased out of more affluent areas.

Emmerson said: "The radical reform to council tax benefit is probably the one that raises the most concerns. Those in favour of greater localism may be pleased that greater powers are being transferred to local authorities.

"It will make the benefits system more complex and less transparent. It will also make it harder to make the benefit system fit together better as a whole. The incentive it provides to local authorities to encourage low-income people to move elsewhere is undesirable."

Universal credit

The IFS said the government had chosen to undermine its move to a universal benefit system before the blueprint was even dry. Scrapping council tax benefit as a centrally designed system and handing it over to councils created a chaotic landscape that universal benefit designers would be hard pressed to incorporate.

If a benefit claimant was going to know how much they would gain from moving to employment, it must be transparent which benefits they would lose and by how much. With the potential for more than 100 separate council tax designs, the IFS said it would difficult to show the gains to be made from taking a job.

Emmerson said: "Moving to a universal benefit structure is undermined somewhat by allowing councils to design their own council tax benefit."

NHS

Sweeping changes to the way the NHS is run will take place while the government imposes unprecedented cuts in spending. The IFS said the NHS was getting a real terms increase of 0.1% but referred to a piece of work they had done with the King's Fund which called for the NHS to get a 1% rise if it is to keep pace with an ageing population and the rising cost of drugs – the coalition's stated aim.

Child benefit cut

When the cut to child benefit for higher rate tax payers takes affect in 2013, it is clear many middle to high income earners will lose out. The IFS said it was concerned the measure was crudely implemented and appeared to contradict some of the government stated aims.

It joined other groups in questioning why the government felt unable to spend the money designing a fairer system that avoided punishing one income families living on a salary of £44,000, who lost the benefit, and two income families where each workers kept their income below the higher rate threshold.

An estimate by the Treasury that tax planning by people just above the threshold would cost £280m in lost tax appeared to just the kind of "inefficiency" the government wanted to avoid, the IFS said.

Maintaining child benefit for standard rate taxpayers and abolishing the education maintenance allowance also appeared to undermine efforts to keep children in school.

Browne said previous research by the IFS showed the allowance was effective in keeping 16- to 18-year-olds in school, especially those of non-working parents, while child benefit for people higher up the income scale was unlikely to have the same effect.

• This article was amended on 22 October 2010. The original said a projection drawn up by civil servants at the Department for Education suggested 40% of teachers could lose their jobs over the course of the spending review. That figure has been corrected to 40,000.